They already took care of V'ger in one of the comics. Spock may want to keep some things to himself, but helping them make an antimatter mine for the Doomsday Machine and Amoeba, and have Humpback Whale linguacode for the Probe would solve those.
As much as I love ST, I don't read comics. Novels yes, but those are not canon. I would think the same is true of comics. But for the average movie goer, they could care less. But those of us who love the SciFi aspect of ST, we want a little realism with explaining away the aspects that should not be effected by Nero.